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Question: Why isn't my .bed file being read as an ASCII file?
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gravatar for thomc
3.6 years ago by
thomc • 0
United States
thomc • 0 wrote:

I just ran MACS peak calling on a bedgraph file, so I've got output as txt.bed

I did this for 6 separate ChIPSeq datasets and when I run GREGOR to look for snp enrichment within a given ChIPSeq dataset, it works for 5/6. However, I keep getting an error message telling me that 1 file "is not an ASCII file". Any ideas how to fix this??? I'm not sure what I could have done during export since I simply used the command line in Unix to wget [file link].

 

Thanks!!!
 
ascii download upload datasets md5 • 862 views
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modified 3.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.6 years ago by thomc • 0
0
gravatar for Jennifer Hillman Jackson
3.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

First (and I know this seems obvious) - double check the MACS output. Was the run actually successful with peaks called? Next, check the download. Comparing a md5 on the version in Galaxy and md5 of what was downloaded will inform if both are an exact match. In Galaxy, the tool to use for this is "Secure Hash / Message Digest". If that is not a match, download again and see if that resolves the issue. 

Thanks, Jen, Galaxy team
ADD COMMENT • link modified 3.6 years ago • written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks Jen!

Chris

ADD REPLY • link written 3.6 years ago by thomc • 0
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